eDNA as a non-invasive tool for species distribution: pipeline validation by mock communities and dispersal dynamics in marine environments

Environmental DNA (eDNA) is a non-invasive and cost-effective molecular approach that has acquired importance over the last decade, growing quickly along with laboratory and sequencing techniques. Despite its widespread application, there’s a lack of standardized and shared protocols. We developed and validated internal protocols using mock communities, and we applied them into the real semi-controlled marine environment of an Atlantic salmon fish farm in the west of Ireland. We tested the protocols and investigated the chance of Salmo salar (Atlantic salmon) DNA detection and transport, by filtering 5L of water in triplicates from inside the fish cages and from the shore. The sampling was conducted in November 2023 and then repeated in May 2024 including intermediate points between cages and shores and during high and low tides. While collecting water, a metaprobe [1] was also deployed to compare active and passive sampling. DNA from filters and metaprobes was extracted with Blood & Tissue (BT) and Power Water (PW) kits (Qiagen). The 12S ribosomal RNA (rRNA) library was prepared with a two-step approach, and samples were pooled after indexing and sequenced on MiSeq (2X250PE) and Next2000 (2X300PE) Illumina sequencers. Demultiplexed sequences were processed with ObiTools launched in Galaxy.eu [2]. Atlantic salmon DNA was successfully detected at the cages with both active and passive sampling in November and May. Interestingly, while no records were reported from the shore in November (except for one filter replicate), Atlantic salmon was detected in filters and metaprobes collected in May during low and high tides. The stage of development and biological activity of salmons (2 kg body weight in November, 6-8 kg in May) and the water temperature (respectively 11.5 and 13.37°C), may have influenced the shedding rate, increasing the chances of DNA detection; on the contrary, tidal movement appeared to not affect the rate of detection.